oneChannelGUI
(last update 19/03/2013)

Install python and HTSeq
Install perl
Install R 2.15.3 (www.r-project.org).
The installation of latest Bioconductor with all packages needed for the course is done run an R shell and writing the following code:

source("http://bioconductor.org/biocLite.R")
biocLite(c("Biobase", "limma", "affylmGUI", "tkWidgets", "GOstats", "AnnotationDbi", "preprocessCore", "IRanges", "baySeq", "Rsamtools", "R.utils", "annotate", "genefilter", "maSigPro", "pamr", "pdmclass", "ChIPpeakAnno", "chipseq", "BSgenome", "Rgraphviz", "affy" ,"annaffy", "affyPLM", "multtest", "ssize", "sizepower", "siggenes", "RankProd", "org.Hs.eg.db", "org.Mm.eg.db", "org.Rn.eg.db", "edgeR",  "metaArray", "MergeMaid", "biomaRt", "GenomeGraphs","AffyCompatible", "Biostrings", "rtracklayer", "Genominator", "hugene10sttranscriptcluster.db", "mogene10sttranscriptcluster.db", "ragene10sttranscriptcluster.db", "HuExExonProbesetLocation", "MoExExonProbesetLocation", "RaExExonProbesetLocation", "snow", "RmiR", "RmiR.Hs.miRNA", "R.utils", "EDASeq","DESeq", "DEXSeq","goseq", "BSgenome.Hsapiens.UCSC.hg19", "TxDb.Hsapiens.UCSC.hg19.knownGene", "oneChannelGUI","chimera", "cummeRbund"))

When installation is finished.
  You can load the library(oneChannelGUI).
To start oneChannelGUI follow the instruction given int the first set of course slides or in the oneChannelGUI user guide.
All NGS tools external to Bioconductor can be installed using oneChannelGUI functionalities, please read the vignettes.

In order to use MIDAS from APT tools for exon array analysis the APT tool version 1.12.0
has  to be used:
http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx?hightlight=true&rootCategoryId=34002#1_3
This because MIDAS was not included in subsequent version since it was not changed.

Windows users:
For the correct installation of Rgraphviz , a library used for GO network visualization it is necessary:
Go to: http://www.stats.ox.ac.uk/~ripley/Win64/W64porting.html , which has a link to
a 64-bit abridged version of graphviz which has been built for 64-bit windows.

1. Extracted the archive
(http://www.stats.ox.ac.uk/pub/Rtools/goodies/Win64No_/) to a folder, eg. C:\graphviz64\graphviz
2. Changed PATH environment variable to point to new location of graphviz
3. used source("http://bioconductor.org/biocLite.R")
biocLite("Rgraphviz") to install the 64-bit binary
4. Restart R






ADDITIONAL INFORMATION
Affymetrix test data sets and exercises
oneChannelGUI tutorial and exercises 1st part
oneChannelGUI tutorial and exercises 2nd part
Set of data to test the functionalities of oneChannelGUI
3IVT two class unpaired test set to test oneChannelGUI statistical tests, filtering, etc.
Data set derved from processed data file from E-TABM-158 ArrayExpress data set to test oneChannelGUI classification modules
Two GEO data sets to test oneChannelGUI statistical tests, filtering, etc.
Tab delimited file data set, based on moe4302, to test oneChannelGUI statistical tests, filtering, etc
Time course data set to test maSigPro implementation of oneChannelGUI
Hs/Mm/Rat two class unpaired data sets to test oneChannelGUI exon modules